Structural Insights into Substrate Specificity and theantiβ-Elimination Mechanism of Pectate Lyase

Biochemistry ◽  
2010 ◽  
Vol 49 (3) ◽  
pp. 539-546 ◽  
Author(s):  
Arefeh Seyedarabi ◽  
Teng Teng To ◽  
Salyha Ali ◽  
Syeed Hussain ◽  
Markus Fries ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Pectate Lyase ◽  
Elimination Mechanism ◽  
Structural Insights

Structural insights into the substrate specificity of a glycoside hydrolase family 5 lichenase from Caldicellulosiruptor sp. F32

2017 ◽  
Vol 474 (20) ◽  
pp. 3373-3389 ◽  
Author(s):  
Dong-Dong Meng ◽  
Xi Liu ◽  
Sheng Dong ◽  
Ye-Fei Wang ◽  
Xiao-Qing Ma ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Substrate Specificity ◽  
Glycoside Hydrolase ◽  
Complex Structure ◽  
Dynamics Simulation ◽  
Structural Basis ◽  
Glycoside Hydrolase Family ◽  
Substrate Selectivity ◽  
Glucose Residue ◽  
Structural Insights

Glycoside hydrolase (GH) family 5 is one of the largest GH families with various GH activities including lichenase, but the structural basis of the GH5 lichenase activity is still unknown. A novel thermostable lichenase F32EG5 belonging to GH5 was identified from an extremely thermophilic bacterium Caldicellulosiruptor sp. F32. F32EG5 is a bi-functional cellulose and a lichenan-degrading enzyme, and exhibited a high activity on β-1,3-1,4-glucan but side activity on cellulose. Thin-layer chromatography and NMR analyses indicated that F32EG5 cleaved the β-1,4 linkage or the β-1,3 linkage while a 4-O-substitued glucose residue linked to a glucose residue through a β-1,3 linkage, which is completely different from extensively studied GH16 lichenase that catalyses strict endo-hydrolysis of the β-1,4-glycosidic linkage adjacent to a 3-O-substitued glucose residue in the mixed-linked β-glucans. The crystal structure of F32EG5 was determined to 2.8 Å resolution, and the crystal structure of the complex of F32EG5 E193Q mutant and cellotetraose was determined to 1.7 Å resolution, which revealed that the exit subsites of substrate-binding sites contribute to both thermostability and substrate specificity of F32EG5. The sugar chain showed a sharp bend in the complex structure, suggesting that a substrate cleft fitting to the bent sugar chains in lichenan is a common feature of GH5 lichenases. The mechanism of thermostability and substrate selectivity of F32EG5 was further demonstrated by molecular dynamics simulation and site-directed mutagenesis. These results provide biochemical and structural insights into thermostability and substrate selectivity of GH5 lichenases, which have potential in industrial processes.

Structural insights into substrate specificity and solvent tolerance in alcohol dehydrogenase ADH-‘A’ from Rhodococcus ruber DSM 44541

2010 ◽  
Vol 46 (34) ◽  
pp. 6314 ◽  
Author(s):  
Martin Karabec ◽  
Andrzej Łyskowski ◽  
Katharina C. Tauber ◽  
Georg Steinkellner ◽  
Wolfgang Kroutil ◽  
...  
Keyword(s):  
Alcohol Dehydrogenase ◽  
Substrate Specificity ◽  
Solvent Tolerance ◽  
Rhodococcus Ruber ◽  
Structural Insights

Structural insights into the substrate specificity of bacterial copper amine oxidase obtained by using irreversible inhibitors

2011 ◽  
Vol 151 (2) ◽  
pp. 167-178 ◽  
Author(s):  
T. Murakawa ◽  
H. Hayashi ◽  
M. Taki ◽  
Y. Yamamoto ◽  
Y. Kawano ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Amine Oxidase ◽  
Copper Amine Oxidase ◽  
Irreversible Inhibitors ◽  
Structural Insights ◽  
Copper Amine

QM/MM studies on the calcium-assisted β-elimination mechanism of pectate lyase from bacillus subtilis

2016 ◽  
Vol 84 (11) ◽  
pp. 1606-1615 ◽  
Author(s):  
Guangcai Ma ◽  
Wenyou Zhu ◽  
Yongjun Liu
Keyword(s):  
Bacillus Subtilis ◽  
Pectate Lyase ◽  
Elimination Mechanism

scholarly journals Structural Insights into the Substrate Specificity Switch Mechanism of the Type III Protein Export Apparatus

Structure ◽  
2019 ◽  
Vol 27 (6) ◽  
pp. 965-976.e6 ◽  
Author(s):  
Yumi Inoue ◽  
Yuya Ogawa ◽  
Miki Kinoshita ◽  
Naoya Terahara ◽  
Masafumi Shimada ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Protein Export ◽  
Type Iii ◽  
Switch Mechanism ◽  
Structural Insights

Structural Insights into the Substrate Specificity of Acyltransferases from Salinomycin Polyketide Synthase

Biochemistry ◽  
2019 ◽  
Vol 58 (27) ◽  
pp. 2978-2986 ◽  
Author(s):  
Fa Zhang ◽  
Ting Shi ◽  
Huining Ji ◽  
Imtiaz Ali ◽  
Shuxin Huang ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Polyketide Synthase ◽  
Structural Insights

scholarly journals Structural insights into the broad substrate specificity of carboxypeptidase T fromThermoactinomyces vulgaris

FEBS Journal ◽  
2015 ◽  
Vol 282 (7) ◽  
pp. 1214-1224 ◽  
Author(s):  
Valery Kh. Akparov ◽  
Vladimir I. Timofeev ◽  
Ilyas G. Khaliullin ◽  
Vytas Švedas ◽  
Galina G. Chestukhina ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Broad Substrate Specificity ◽  
Structural Insights ◽  
Carboxypeptidase T

scholarly journals Structural Insights into the Substrate Specificity of Human Granzyme H: The Functional Roles of a Novel RKR Motif

2011 ◽  
Vol 188 (2) ◽  
pp. 765-773 ◽  
Author(s):  
Li Wang ◽  
Kai Zhang ◽  
Lianfeng Wu ◽  
Shengwu Liu ◽  
Honglian Zhang ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Functional Roles ◽  
Structural Insights

scholarly journals Structural insights into substrate specificity of isomaltase fromSaccharomyces cerevisiae

2008 ◽  
Vol 64 (a1) ◽  
pp. C258-C258
Author(s):  
K. Yamamoto ◽  
H. Miyake ◽  
M. Kusunoki ◽  
S. Osaki
Keyword(s):  
Substrate Specificity ◽  
Structural Insights
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